Files in jsilve24/fido
Bayesian Multinomial Logistic Normal Regression

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.github/.gitignore

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.github/workflows/pkgdown.yaml

.github/workflows/rhub.yaml

.gitignore

.gitmodules

DESCRIPTION

NAMESPACE

NEWS.md R/R2.R R/RISK_CCFA.R R/RcppExports.R R/bassetfit_s3.R R/driver-utils.R R/fido.R R/fido_transforms.R R/fido_utils.R R/fidofit_methods.R R/fidofit_s3.R R/fit_basset.R R/fit_maltipoo.R R/fit_orthus.R R/fit_pibble.R R/generics_s3.R R/iqlr.R R/kernels.R R/mallard-data.R R/mallard_family-data.R R/maltipoo_sim.R R/maltipoofit_s3.R R/orthus_sim.R R/orthus_transform_wrapper.R R/pcrbias_mock-data.R R/pibble_plotting.R R/pibble_sim.R README.md

_pkgdown.yml

cleanup

configure

configure.ac

data/RISK_CCFA.RData

data/mallard.RData

data/mallard_family.RData

data/pcrbias_mock.RData

docs/404.html

docs/articles/index.html

docs/articles/introduction-to-fido.html

docs/articles/mitigating-pcrbias.html

docs/articles/non-linear-models.html

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fido.Rproj

inst/CITATION

inst/extdata/Kashyap2013/README.txt

inst/extdata/Kashyap2013/metabolites.csv

inst/extdata/Kashyap2013/microbe.rda

inst/fido.png

inst/include/AdamOptim.h

inst/include/LaplaceApproximation.h

inst/include/MaltipooCollapsed.h

inst/include/MatDist.h

inst/include/MatDist_thread.h

inst/include/MatrixAlgebra.h

inst/include/MongrelModelClass.h

inst/include/MultDirichletBoot.h

inst/include/PibbleCollapsed.h

inst/include/SpecialFunctions.h

inst/include/fido.h

inst/include/fidoGenerated.h.in

maintainer.tex

man/RISK_CCFA.Rd man/RISK_CCFA_otu.Rd man/RISK_CCFA_sam.Rd man/RISK_CCFA_tax.Rd man/Y.Rd man/access_dims.Rd man/alr.Rd man/alrInv.Rd man/alrInv_array.Rd man/alr_array.Rd man/as.list.orthusfit.Rd man/as.list.pibblefit.Rd man/as.orthusfit.Rd man/as.pibblefit.Rd man/basset_fit.Rd man/check_dims.Rd man/clr_array.Rd man/coef.orthusfit.Rd man/coef.pibblefit.Rd man/conjugateLinearModel.Rd man/convert_orthus_covariance.Rd man/create_default_ilr_base.Rd man/fido_package.Rd man/fido_transforms.Rd man/gather_array.Rd man/kernels.Rd man/lambda_to_iqlr.Rd man/lmvgamma.Rd man/lmvgamma_deriv.Rd man/loglikPibbleCollapsed.Rd man/mallard.Rd man/mallard_family.Rd man/metadata.Rd man/miniclo.Rd man/miniclo_array.Rd man/mongrel-deprecated.Rd man/name.Rd man/name.orthusfit.Rd man/name.pibblefit.Rd man/name_dims.Rd man/optimPibbleCollapsed.Rd man/orthus_fit.Rd man/orthus_lr_transforms.Rd man/orthus_sim.Rd man/orthus_tidy_samples.Rd man/orthusfit.Rd man/pcrbias_mock.Rd man/pibble_fit.Rd man/pibble_sim.Rd man/pibble_tidy_samples.Rd man/pibblefit.Rd man/plot.pibblefit.Rd man/ppc.Rd man/ppc.pibblefit.Rd man/ppc_summary.Rd man/predict.bassetfit.Rd man/predict.pibblefit.Rd man/print.orthusfit.Rd man/print.pibblefit.Rd man/r2.Rd man/random_pibble_init.Rd man/refit.Rd man/req.Rd man/req.orthusfit.Rd man/req.pibblefit.Rd man/sample_prior.Rd man/sample_prior.pibblefit.Rd man/store_coord.Rd man/summarise_posterior.Rd man/summary.orthusfit.Rd man/summary.pibblefit.Rd man/uncollapsePibble.Rd man/uncollapsePibble_sigmaKnown.Rd man/verify.Rd man/verify.bassetfit.Rd man/verify.orthusfit.Rd man/verify.pibblefit.Rd

src/ConjugateLinearModel.cpp

src/Makevars.in

src/Makevars.win

src/MaltipooCollapsed_LGH.cpp

src/MaltipooCollapsed_Optim.cpp

src/MatrixAlgebra.cpp

src/PibbleCollapsed_LGH.cpp

src/PibbleCollapsed_Optim.cpp

src/PibbleCollapsed_Uncollapse.cpp

src/PibbleCollapsed_Uncollapse_sigmaKnown.cpp

src/RcppExports.cpp

src/SpecialFunctions.cpp

src/test_LaplaceApproximation.cpp

src/test_MultDirichletBoot.cpp

src/test_utils.cpp

tests/testthat.R

tests/testthat/.gitignore

vignettes/.gitignore

vignettes/bibliography.bib

vignettes/fido-lambda-all.png

vignettes/fido-lambda-cd.png

vignettes/fido-lambda-res.png

vignettes/fido-ppc-scratch.png

vignettes/fido-ppc.png

vignettes/introduction-to-fido.Rmd

vignettes/introduction-to-fido.Rmd.orig

vignettes/mitigating-pcrbias.Rmd

vignettes/mitigating-pcrbias.Rmd.orig

vignettes/non-linear-models.Rmd

vignettes/orthus-prior-structure.png

vignettes/orthus.Rmd

vignettes/orthus.Rmd.orig

vignettes/pcr-clr-cycle-num.png

vignettes/pcr-max-lik.png

vignettes/pcr-model-results.png

vignettes/pcr-results-cycle-num.png

vignettes/pcrbias_summary_graphic.png

vignettes/pibble-CD-clr.png

vignettes/pibble-posterior-summary.png

vignettes/pibble-ppc-sum.png

vignettes/pibble-ppc.png

vignettes/pibble-priors.png

vignettes/picking_priors.Rmd

jsilve24/fido documentation built on Feb. 27, 2025, 11:48 a.m.

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jsilve24/fido
Bayesian Multinomial Logistic Normal Regression

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Bayesian Multinomial Logistic Normal Regression

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Bayesian Multinomial Logistic Normal Regression

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Bayesian Multinomial Logistic Normal Regression